Fuzzy regex matching with python returns empty list

Question

I have made a clumsy first attempt at fuzzy pattern matching using the re module in python 2.7.

Unfortunately every attempt I make returns an empty list. I simply don't understand the syntax required. I was wondering if someone might tell me why the following code:

import re
m = re.findall('(ATCT){e<=1}', 'ATCGATCGGCATGCAGTGCAGAAGTGACGAT')
print m

returns an empty list?

Are you only interested in the explanation? Not in a solution? Your regex is a mess. It matches ATCT followed with {e<=1} - these are literal character sequences. See what it matches. — Wiktor Stribiżew
– Wiktor Stribiżew, Commented Feb 17, 2016 at 11:28
@AvinashRaj the pattern should match to several places in the string with one match, the output should be a list of those patterns. — poppyseeds
– poppyseeds, Commented Feb 17, 2016 at 11:29
If you are interested in a solution, please explain - illustrate - what you need to obtain. — Wiktor Stribiżew
– Wiktor Stribiżew, Commented Feb 17, 2016 at 11:31

Wiktor Stribiżew · Accepted Answer · 2016-02-17 12:02:25Z

2

Since you intended to use the PyPi regex module, you need to use

>>> import regex
>>> m = regex.findall('(ATCT){e<=1}', 'ATCGATCGGCATGCAGTGCAGAAGTGACGAT')
>>> print(m)
['ATCG', 'ATCG']

answered Feb 17, 2016 at 12:02

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Wiktor Stribiżew

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2 Comments

poppyseeds Over a year ago

Thank you. I did not realise they were different modules as I was unaware of the difference. As a follow up question, is there a way to perform this using the re module?

Wiktor Stribiżew Over a year ago

There is no way to do that with the re module.

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